Starting phenix.real_space_refine
on Tue Feb  3 20:25:57 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/9uyl_64614/02_2026/9uyl_64614.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9uyl_64614/02_2026/9uyl_64614.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9uyl_64614/02_2026/9uyl_64614.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9uyl_64614/02_2026/9uyl_64614.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9uyl_64614/02_2026/9uyl_64614.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9uyl_64614/02_2026/9uyl_64614.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.030
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      18      5.16       5
     C    4181      2.51       5
     N    1124      2.21       5
     O    1259      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6588
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "R"
      Number of atoms: 1602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 246, 1602
          Classifications: {'peptide': 246}
          Incomplete info: {'truncation_to_alanine': 106}
          Link IDs: {'PTRANS': 9, 'TRANS': 236}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 474
          Unresolved non-hydrogen angles: 625
          Unresolved non-hydrogen dihedrals: 419
          Unresolved non-hydrogen chiralities: 52
          Planarities with less than four sites: {'TYR:plan': 7, 'PHE:plan': 16, 'ASN:plan1': 5, 'TRP:plan': 5, 'ASP:plan': 1, 'HIS:plan': 4, 'ARG:plan': 4, 'GLN:plan1': 1, 'TPO:plan-1': 2}
          Unresolved non-hydrogen planarities: 254
    Chain: "L"
      Number of atoms: 83
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 83
          Classifications: {'peptide': 10}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 8}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 2436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 323, 2436
          Classifications: {'peptide': 323}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PTRANS': 25, 'TRANS': 297}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 151
          Unresolved non-hydrogen angles: 180
          Unresolved non-hydrogen dihedrals: 127
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 7, 'ASN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 102
    Chain: "B"
      Number of atoms: 781
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 781
          Classifications: {'peptide': 109}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 2, 'TRANS': 106}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 49
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 31
    Chain: "C"
      Number of atoms: 1686
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1686
          Classifications: {'peptide': 222}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 8, 'TRANS': 213}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 13
  Time building chain proxies: 1.74, per 1000 atoms: 0.26
  Number of scatterers: 6588
  At special positions: 0
  Unit cell: (81.396, 101.745, 142.443, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      18     16.00
     P       6     15.00
     O    1259      8.00
     N    1124      7.00
     C    4181      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 110 " - pdb=" SG  CYS R 187 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  24 " - pdb=" SG  CYS C  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 146 " - pdb=" SG  CYS C 220 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.67
  Conformation dependent library (CDL) restraints added in 267.7 milliseconds
  

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1714

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 12 sheets defined
      24.0% alpha, 21.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'R' and resid 42 through 65
      removed outlier: 4.259A  pdb=" N   CYS R  46 " --> pdb=" O   LEU R  42 " (cutoff:3.500A)
      Proline residue:  R  54  - end of helix
      removed outlier: 3.874A  pdb=" N   ILE R  60 " --> pdb=" O   ASN R  56 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   TRP R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   PHE R  62 " --> pdb=" O   ILE R  58 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 70 through 88
    Processing helix  chain 'R' and resid 89 through 98
    Processing helix  chain 'R' and resid 105 through 108
      removed outlier: 3.853A  pdb=" N   TRP R 108 " --> pdb=" O   PHE R 105 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 105 through 108'
    Processing helix  chain 'R' and resid 109 through 141
      removed outlier: 3.718A  pdb=" N   LEU R 139 " --> pdb=" O   HIS R 135 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   HIS R 141 " --> pdb=" O   ILE R 137 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 150 through 174
      Proline residue:  R 171  - end of helix
      removed outlier: 3.867A  pdb=" N   TYR R 174 " --> pdb=" O   GLY R 170 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 202 through 215
      removed outlier: 3.828A  pdb=" N   LEU R 206 " --> pdb=" O   ARG R 202 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   THR R 207 " --> pdb=" O   HIS R 203 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 215 through 227
      removed outlier: 3.572A  pdb=" N   LEU R 220 " --> pdb=" O   LEU R 216 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 253 through 276
      removed outlier: 3.683A  pdb=" N   THR R 260 " --> pdb=" O   VAL R 256 " (cutoff:3.500A)
      Proline residue:  R 261  - end of helix
      removed outlier: 4.217A  pdb=" N   ASN R 275 " --> pdb=" O   THR R 271 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 285 through 304
      Proline residue:  R 301  - end of helix
    Processing helix  chain 'A' and resid 98 through 109
    Processing helix  chain 'A' and resid 159 through 163
    Processing helix  chain 'B' and resid 86 through 90
      removed outlier: 4.109A  pdb=" N   THR B  90 " --> pdb=" O   PRO B  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 84
      removed outlier: 3.872A  pdb=" N   PHE C  84 " --> pdb=" O   PRO C  81 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 211 through 215
      removed outlier: 4.203A  pdb=" N   THR C 215 " --> pdb=" O   ALA C 212 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'R' and resid 1360 through 1362
      removed outlier: 3.757A  pdb=" N   VAL A  20 " --> pdb=" O   LYS A  11 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLY A  39 " --> pdb=" O   PHE A 115 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   VAL A  41 " --> pdb=" O   TYR A 113 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   TYR A 113 " --> pdb=" O   VAL A  41 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28
      removed outlier: 3.614A  pdb=" N   VAL A 171 " --> pdb=" O   PHE A  27 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   TYR A 144 " --> pdb=" O   ILE A 168 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   TYR A  54 " --> pdb=" O   PHE A 149 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   VAL A  84 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   LEU A  57 " --> pdb=" O   ALA A  82 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ALA A  82 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 129
    Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 186
      removed outlier: 3.801A  pdb=" N   ALA A 201 " --> pdb=" O   ALA A 184 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   THR A 186 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   SER A 202 " --> pdb=" O   ASN A 217 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   VAL A 216 " --> pdb=" O   TYR A 272 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 208
      removed outlier: 3.525A  pdb=" N   VAL A 343 " --> pdb=" O   LEU A 327 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   VAL A 345 " --> pdb=" O   VAL A 325 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   VAL A 325 " --> pdb=" O   VAL A 345 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   PHE A 349 " --> pdb=" O   TYR A 321 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   TYR A 321 " --> pdb=" O   PHE A 349 " (cutoff:3.500A)
      removed outlier: 7.649A  pdb=" N   LEU A 351 " --> pdb=" O   VAL A 319 " (cutoff:3.500A)
      removed outlier: 9.617A  pdb=" N   VAL A 319 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   VAL A 328 " --> pdb=" O   LYS A 230 " (cutoff:3.500A)
      removed outlier: 4.396A  pdb=" N   LYS A 230 " --> pdb=" O   VAL A 328 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   ALA A 258 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ILE A 233 " --> pdb=" O   GLU A 256 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ALA A 254 " --> pdb=" O   VAL A 235 " (cutoff:3.500A)
      removed outlier: 7.612A  pdb=" N   GLN A 237 " --> pdb=" O   PRO A 252 " (cutoff:3.500A)
      removed outlier: 7.412A  pdb=" N   ALA A 239 " --> pdb=" O   LYS A 250 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   LYS A 250 " --> pdb=" O   ALA A 239 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 12
      removed outlier: 3.732A  pdb=" N   THR B 108 " --> pdb=" O   TYR B  93 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 67 through 72
    Processing sheet with id=AA8, first strand: chain 'C' and resid 5 through 6
    Processing sheet with id=AA9, first strand: chain 'C' and resid 11 through 12
      removed outlier: 3.665A  pdb=" N   TYR C  37 " --> pdb=" O   TYR C  88 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   TRP C  36 " --> pdb=" O   LEU C  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 20 through 23
      removed outlier: 3.517A  pdb=" N   THR C  73 " --> pdb=" O   SER C  66 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   SER C  66 " --> pdb=" O   THR C  73 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 128 through 131
      removed outlier: 3.822A  pdb=" N   LEU C 142 " --> pdb=" O   MET C 207 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   MET C 207 " --> pdb=" O   LEU C 142 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 181 through 184
      removed outlier: 6.821A  pdb=" N   TRP C 160 " --> pdb=" O   VAL C 172 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   SER C 174 " --> pdb=" O   ILE C 158 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   ILE C 158 " --> pdb=" O   SER C 174 " (cutoff:3.500A)
      removed outlier: 6.011A  pdb=" N   SER C 176 " --> pdb=" O   SER C 156 " (cutoff:3.500A)
      removed outlier: 8.747A  pdb=" N   SER C 156 " --> pdb=" O   SER C 176 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   TYR C 233 " --> pdb=" O   ARG C 222 " (cutoff:3.500A)
      removed outlier: 7.974A  pdb=" N   ARG C 224 " --> pdb=" O   LEU C 231 " (cutoff:3.500A)
      removed outlier: 8.068A  pdb=" N   LEU C 231 " --> pdb=" O   ARG C 224 " (cutoff:3.500A)

    249 hydrogen bonds defined for protein.
    678 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.93

  Time building geometry restraints manager: 0.85 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.34: 2119
        1.34 -     1.46: 1644
        1.46 -     1.58: 2926
        1.58 -     1.71: 22
        1.71 -     1.83: 23
  Bond restraints: 6734
  Sorted by residual:
  bond pdb=" OG1 TPO R1360 "
       pdb=" P   TPO R1360 "
    ideal  model  delta    sigma   weight residual
    1.717  1.609  0.108 2.00e-02 2.50e+03 2.90e+01
  bond pdb=" OG1 TPO R1359 "
       pdb=" P   TPO R1359 "
    ideal  model  delta    sigma   weight residual
    1.717  1.610  0.107 2.00e-02 2.50e+03 2.87e+01
  bond pdb=" O2P TPO R1359 "
       pdb=" P   TPO R1359 "
    ideal  model  delta    sigma   weight residual
    1.528  1.611 -0.083 2.00e-02 2.50e+03 1.73e+01
  bond pdb=" O3P TPO R1359 "
       pdb=" P   TPO R1359 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.69e+01
  bond pdb=" O2P TPO R1360 "
       pdb=" P   TPO R1360 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.68e+01
  ... (remaining 6729 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.53: 9088
        2.53 -     5.06: 117
        5.06 -     7.59: 12
        7.59 -    10.13: 3
       10.13 -    12.66: 2
  Bond angle restraints: 9222
  Sorted by residual:
  angle pdb=" CB  TPO R1359 "
        pdb=" OG1 TPO R1359 "
        pdb=" P   TPO R1359 "
      ideal   model   delta    sigma   weight residual
     119.31  106.65   12.66 3.00e+00 1.11e-01 1.78e+01
  angle pdb=" CB  TPO R1360 "
        pdb=" OG1 TPO R1360 "
        pdb=" P   TPO R1360 "
      ideal   model   delta    sigma   weight residual
     119.31  106.80   12.51 3.00e+00 1.11e-01 1.74e+01
  angle pdb=" N   GLU R 269 "
        pdb=" CA  GLU R 269 "
        pdb=" CB  GLU R 269 "
      ideal   model   delta    sigma   weight residual
     110.28  115.66   -5.38 1.55e+00 4.16e-01 1.21e+01
  angle pdb=" N   THR A 224 "
        pdb=" CA  THR A 224 "
        pdb=" C   THR A 224 "
      ideal   model   delta    sigma   weight residual
     108.24  112.60   -4.36 1.32e+00 5.74e-01 1.09e+01
  angle pdb=" OG1 TPO R1359 "
        pdb=" P   TPO R1359 "
        pdb=" O1P TPO R1359 "
      ideal   model   delta    sigma   weight residual
     100.43  109.69   -9.26 3.00e+00 1.11e-01 9.53e+00
  ... (remaining 9217 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.11: 3545
       15.11 -    30.22: 305
       30.22 -    45.34: 79
       45.34 -    60.45: 11
       60.45 -    75.56: 9
  Dihedral angle restraints: 3949
    sinusoidal: 1300
      harmonic: 2649
  Sorted by residual:
  dihedral pdb=" CB  CYS R 110 "
           pdb=" SG  CYS R 110 "
           pdb=" SG  CYS R 187 "
           pdb=" CB  CYS R 187 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   59.41   33.59     1      1.00e+01 1.00e-02 1.60e+01
  dihedral pdb=" CA  LEU R 109 "
           pdb=" C   LEU R 109 "
           pdb=" N   CYS R 110 "
           pdb=" CA  CYS R 110 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.36  -18.64     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" CG  ARG C 191 "
           pdb=" CD  ARG C 191 "
           pdb=" NE  ARG C 191 "
           pdb=" CZ  ARG C 191 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -132.18   42.18     2      1.50e+01 4.44e-03 9.62e+00
  ... (remaining 3946 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 670
       0.029 -    0.059: 252
       0.059 -    0.088: 91
       0.088 -    0.117: 66
       0.117 -    0.146: 8
  Chirality restraints: 1087
  Sorted by residual:
  chirality pdb=" CA  THR R 185 "
            pdb=" N   THR R 185 "
            pdb=" C   THR R 185 "
            pdb=" CB  THR R 185 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.15 2.00e-01 2.50e+01 5.34e-01
  chirality pdb=" CB  THR A 227 "
            pdb=" CA  THR A 227 "
            pdb=" OG1 THR A 227 "
            pdb=" CG2 THR A 227 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.42    0.13 2.00e-01 2.50e+01 4.19e-01
  chirality pdb=" CA  ILE C  49 "
            pdb=" N   ILE C  49 "
            pdb=" C   ILE C  49 "
            pdb=" CB  ILE C  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.16e-01
  ... (remaining 1084 not shown)

  Planarity restraints: 1175
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN R 118 "   -0.011 2.00e-02 2.50e+03   2.24e-02 5.03e+00
        pdb=" C   GLN R 118 "    0.039 2.00e-02 2.50e+03
        pdb=" O   GLN R 118 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   LEU R 119 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA R 117 "    0.011 2.00e-02 2.50e+03   2.15e-02 4.63e+00
        pdb=" C   ALA R 117 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   ALA R 117 "    0.014 2.00e-02 2.50e+03
        pdb=" N   GLN R 118 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 128 "   -0.010 2.00e-02 2.50e+03   1.93e-02 3.74e+00
        pdb=" C   LEU R 128 "    0.033 2.00e-02 2.50e+03
        pdb=" O   LEU R 128 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   THR R 129 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1172 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 983
        2.76 -     3.29: 6371
        3.29 -     3.83: 10483
        3.83 -     4.36: 11458
        4.36 -     4.90: 20369
  Nonbonded interactions: 49664
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 227 "
            pdb=" O   VAL A 262 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" O   MET R 121 "
            pdb=" OG  SER R 124 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" OG  SER C  64 "
            pdb=" OG1 THR C  75 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" OG  SER A  13 "
            pdb=" OD1 ASN A  15 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" OG  SER A 303 "
            pdb=" OG1 THR A 350 "
     model   vdw
     2.268 3.040
  ... (remaining 49659 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.040
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6639
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.108   6738  Z= 0.207
  Angle     :  0.726  12.657   9230  Z= 0.394
  Chirality :  0.041   0.146   1087
  Planarity :  0.004   0.041   1175
  Dihedral  : 12.882  75.561   2223
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.26 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.50 (0.28), residues: 872
  helix:  0.10 (0.39), residues: 175
  sheet: -0.11 (0.34), residues: 254
  loop : -2.05 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 143 
 TYR   0.007   0.001   TYR C  92 
 PHE   0.016   0.001   PHE R  62 
 TRP   0.009   0.001   TRP R  75 
 HIS   0.002   0.001   HIS R 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 6734)
  covalent geometry    : angle       0.72602 ( 9222)
  SS BOND              : bond        0.00340 (    4)
  SS BOND              : angle       1.05642 (    8)
  hydrogen bonds       : bond        0.24946 (  249)
  hydrogen bonds       : angle       8.95353 (  678)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
REVERT: R  118 GLN cc_start: 0.8646 (tp-100) cc_final: 0.8182 (tp40)
REVERT: R  183 ASN cc_start: 0.7941 (m-40) cc_final: 0.7338 (p0)
REVERT: R  229 LEU cc_start: 0.3984 (tp) cc_final: 0.3534 (mt)
REVERT: A  113 TYR cc_start: 0.8094 (m-80) cc_final: 0.7251 (m-80)
REVERT: A  364 GLU cc_start: 0.8333 (pm20) cc_final: 0.7744 (pm20)
REVERT: C  214 ASP cc_start: 0.6685 (m-30) cc_final: 0.6438 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.0725
  time to fit residues: 15.9660
Evaluate side-chains
  110 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.8986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
R 118 GLN
A 299 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.192640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.158280 restraints weight = 10019.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.4151 rms_B_bonded: 2.98
r_work: 0.3898 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.1809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   6738  Z= 0.158
  Angle     :  0.651   7.762   9230  Z= 0.333
  Chirality :  0.045   0.166   1087
  Planarity :  0.004   0.044   1175
  Dihedral  :  4.557  51.874    975
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  8.83 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 11.78 %
    Favored  : 86.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.08 (0.29), residues: 872
  helix:  1.05 (0.40), residues: 170
  sheet: -0.10 (0.34), residues: 258
  loop : -1.87 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 224 
 TYR   0.011   0.001   TYR R 188 
 PHE   0.024   0.002   PHE A 268 
 TRP   0.010   0.001   TRP C 227 
 HIS   0.005   0.001   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 6734)
  covalent geometry    : angle       0.65011 ( 9222)
  SS BOND              : bond        0.00604 (    4)
  SS BOND              : angle       1.21855 (    8)
  hydrogen bonds       : bond        0.04198 (  249)
  hydrogen bonds       : angle       6.15369 (  678)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 119
  time to evaluate  : 0.263 
Fit side-chains
REVERT: R  118 GLN cc_start: 0.8670 (tp40) cc_final: 0.8105 (tp-100)
REVERT: R  122 PHE cc_start: 0.8974 (m-10) cc_final: 0.8485 (m-10)
REVERT: R  183 ASN cc_start: 0.7857 (m-40) cc_final: 0.7305 (p0)
REVERT: R  229 LEU cc_start: 0.4183 (tp) cc_final: 0.3623 (mt)
REVERT: A  113 TYR cc_start: 0.8378 (m-80) cc_final: 0.8138 (m-80)
REVERT: C   83 ASP cc_start: 0.7061 (m-30) cc_final: 0.6155 (m-30)
REVERT: C  214 ASP cc_start: 0.6890 (m-30) cc_final: 0.6578 (m-30)
  outliers start: 13
  outliers final: 8
  residues processed: 128
  average time/residue: 0.0614
  time to fit residues: 11.5203
Evaluate side-chains
  112 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain L residue  130 PHE
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain C residue  161 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 1 optimal weight:    8.9990
   chunk 66 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 84 optimal weight:    6.9990
   chunk 53 optimal weight:    2.9990
   chunk 14 optimal weight:   10.0000
   chunk 73 optimal weight:    5.9990
   chunk 58 optimal weight:    0.5980
   chunk 9 optimal weight:    5.9990
   chunk 12 optimal weight:    6.9990
   overall best weight:    2.2786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 210 HIS
B  83 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.183558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.147850 restraints weight = 10023.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.4016 rms_B_bonded: 3.68
r_work: 0.3672 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.2780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049   6738  Z= 0.285
  Angle     :  0.751  10.289   9230  Z= 0.385
  Chirality :  0.047   0.170   1087
  Planarity :  0.005   0.044   1175
  Dihedral  :  5.014  36.305    975
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  : 10.89 %
    Favored  : 88.99 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 16.40 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.24 (0.29), residues: 872
  helix:  1.10 (0.40), residues: 173
  sheet: -0.32 (0.33), residues: 272
  loop : -2.04 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 224 
 TYR   0.015   0.002   TYR A 321 
 PHE   0.027   0.002   PHE A  61 
 TRP   0.018   0.002   TRP C 171 
 HIS   0.005   0.002   HIS A 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00677 ( 6734)
  covalent geometry    : angle       0.75110 ( 9222)
  SS BOND              : bond        0.00708 (    4)
  SS BOND              : angle       1.09516 (    8)
  hydrogen bonds       : bond        0.04196 (  249)
  hydrogen bonds       : angle       6.02802 (  678)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 103
  time to evaluate  : 0.256 
Fit side-chains
REVERT: R  118 GLN cc_start: 0.8832 (tp40) cc_final: 0.8345 (tp-100)
REVERT: R  122 PHE cc_start: 0.9066 (m-10) cc_final: 0.8449 (m-10)
REVERT: R  183 ASN cc_start: 0.7860 (m-40) cc_final: 0.7258 (p0)
REVERT: R  229 LEU cc_start: 0.4291 (tp) cc_final: 0.3771 (mt)
  outliers start: 25
  outliers final: 15
  residues processed: 120
  average time/residue: 0.0666
  time to fit residues: 11.3158
Evaluate side-chains
  108 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain L residue  130 PHE
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   54 TYR
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain C residue   71 ASP
Chi-restraints excluded: chain C residue  145 SER
Chi-restraints excluded: chain C residue  161 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 18 optimal weight:   20.0000
   chunk 36 optimal weight:    0.5980
   chunk 78 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 24 optimal weight:   10.0000
   chunk 27 optimal weight:    0.2980
   chunk 22 optimal weight:   20.0000
   chunk 48 optimal weight:    3.9990
   chunk 82 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 299 ASN
B  83 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4460 r_free = 0.4460 target = 0.187306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.151126 restraints weight = 10017.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.4056 rms_B_bonded: 3.91
r_work: 0.3714 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.2794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   6738  Z= 0.154
  Angle     :  0.653  11.829   9230  Z= 0.330
  Chirality :  0.045   0.188   1087
  Planarity :  0.004   0.044   1175
  Dihedral  :  4.796  42.102    975
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  9.29 %
    Favored  : 90.60 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 17.68 %
    Favored  : 79.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.17 (0.29), residues: 872
  helix:  1.30 (0.40), residues: 170
  sheet: -0.24 (0.34), residues: 257
  loop : -2.02 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 224 
 TYR   0.018   0.001   TYR C 184 
 PHE   0.015   0.002   PHE R  62 
 TRP   0.013   0.001   TRP C 171 
 HIS   0.003   0.001   HIS A 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 6734)
  covalent geometry    : angle       0.65296 ( 9222)
  SS BOND              : bond        0.00420 (    4)
  SS BOND              : angle       0.69655 (    8)
  hydrogen bonds       : bond        0.03435 (  249)
  hydrogen bonds       : angle       5.60685 (  678)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.264 
Fit side-chains
REVERT: R  118 GLN cc_start: 0.8797 (tp40) cc_final: 0.8271 (tp40)
REVERT: R  122 PHE cc_start: 0.9040 (m-10) cc_final: 0.8290 (m-80)
REVERT: R  183 ASN cc_start: 0.7860 (m-40) cc_final: 0.7330 (p0)
REVERT: R  229 LEU cc_start: 0.4253 (tp) cc_final: 0.3775 (mt)
REVERT: B   89 ASP cc_start: 0.7606 (m-30) cc_final: 0.7304 (m-30)
REVERT: C   83 ASP cc_start: 0.7216 (m-30) cc_final: 0.6492 (m-30)
  outliers start: 19
  outliers final: 13
  residues processed: 109
  average time/residue: 0.0589
  time to fit residues: 9.6436
Evaluate side-chains
  102 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain L residue  130 PHE
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   54 TYR
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue  145 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 72 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 76 optimal weight:    0.7980
   chunk 88 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 57 optimal weight:   10.0000
   chunk 74 optimal weight:    6.9990
   chunk 18 optimal weight:    6.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
R 280 HIS
A 237 GLN
B  83 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.186651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.140854 restraints weight = 10142.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.3904 rms_B_bonded: 2.80
r_work: 0.3745 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.3037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6738  Z= 0.180
  Angle     :  0.665   9.578   9230  Z= 0.335
  Chirality :  0.045   0.172   1087
  Planarity :  0.004   0.045   1175
  Dihedral  :  4.803  39.946    975
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  : 10.21 %
    Favored  : 89.68 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 18.63 %
    Favored  : 77.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.21 (0.29), residues: 872
  helix:  1.24 (0.40), residues: 175
  sheet: -0.38 (0.33), residues: 257
  loop : -1.97 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 224 
 TYR   0.025   0.002   TYR A 321 
 PHE   0.016   0.002   PHE C 226 
 TRP   0.014   0.001   TRP C 171 
 HIS   0.004   0.001   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 6734)
  covalent geometry    : angle       0.66534 ( 9222)
  SS BOND              : bond        0.00471 (    4)
  SS BOND              : angle       0.74738 (    8)
  hydrogen bonds       : bond        0.03304 (  249)
  hydrogen bonds       : angle       5.47507 (  678)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 0.224 
Fit side-chains
REVERT: R  118 GLN cc_start: 0.8875 (tp40) cc_final: 0.8385 (tp40)
REVERT: R  122 PHE cc_start: 0.9029 (m-10) cc_final: 0.8267 (m-80)
REVERT: R  183 ASN cc_start: 0.7811 (m-40) cc_final: 0.7275 (p0)
REVERT: R  188 TYR cc_start: 0.5787 (OUTLIER) cc_final: 0.4660 (t80)
REVERT: R  229 LEU cc_start: 0.3885 (tp) cc_final: 0.3501 (mt)
REVERT: C   83 ASP cc_start: 0.7177 (m-30) cc_final: 0.6489 (m-30)
  outliers start: 23
  outliers final: 14
  residues processed: 113
  average time/residue: 0.0693
  time to fit residues: 11.1335
Evaluate side-chains
  108 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  188 TYR
Chi-restraints excluded: chain R residue  190 ASN
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain L residue  130 PHE
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   54 TYR
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue  145 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 88 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 46 optimal weight:    0.2980
   chunk 9 optimal weight:    7.9990
   chunk 81 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 58 optimal weight:    0.0470
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.5278

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.188323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.156322 restraints weight = 10152.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.4136 rms_B_bonded: 3.09
r_work: 0.3801 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.3065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6738  Z= 0.126
  Angle     :  0.644  12.760   9230  Z= 0.320
  Chirality :  0.044   0.201   1087
  Planarity :  0.004   0.045   1175
  Dihedral  :  4.687  45.134    975
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  9.17 %
    Favored  : 90.71 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 20.06 %
    Favored  : 76.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.13 (0.29), residues: 872
  helix:  1.49 (0.40), residues: 170
  sheet: -0.36 (0.33), residues: 257
  loop : -1.96 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 224 
 TYR   0.022   0.001   TYR A 321 
 PHE   0.013   0.001   PHE R  62 
 TRP   0.011   0.001   TRP C 171 
 HIS   0.003   0.001   HIS A 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6734)
  covalent geometry    : angle       0.64371 ( 9222)
  SS BOND              : bond        0.00334 (    4)
  SS BOND              : angle       0.57624 (    8)
  hydrogen bonds       : bond        0.03052 (  249)
  hydrogen bonds       : angle       5.25488 (  678)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.259 
Fit side-chains
REVERT: R  118 GLN cc_start: 0.8844 (tp40) cc_final: 0.8085 (tp40)
REVERT: R  122 PHE cc_start: 0.9019 (m-10) cc_final: 0.8165 (m-80)
REVERT: R  183 ASN cc_start: 0.7798 (m-40) cc_final: 0.7258 (p0)
REVERT: R  188 TYR cc_start: 0.5796 (OUTLIER) cc_final: 0.4627 (t80)
REVERT: R  213 ILE cc_start: 0.7270 (mm) cc_final: 0.6938 (mt)
REVERT: R  229 LEU cc_start: 0.4075 (tp) cc_final: 0.3788 (mt)
REVERT: A  129 LEU cc_start: 0.7699 (mt) cc_final: 0.7261 (mt)
REVERT: C  214 ASP cc_start: 0.7119 (m-30) cc_final: 0.6795 (m-30)
  outliers start: 19
  outliers final: 12
  residues processed: 114
  average time/residue: 0.0548
  time to fit residues: 9.6194
Evaluate side-chains
  108 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  188 TYR
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain L residue  130 PHE
Chi-restraints excluded: chain A residue   49 LYS
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   54 TYR
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue  161 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 73 optimal weight:    0.1980
   chunk 12 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 22 optimal weight:    9.9990
   chunk 60 optimal weight:    4.9990
   chunk 78 optimal weight:    7.9990
   chunk 66 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 162 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.186618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.154393 restraints weight = 10012.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.4107 rms_B_bonded: 3.11
r_work: 0.3767 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.3180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   6738  Z= 0.154
  Angle     :  0.659  11.037   9230  Z= 0.326
  Chirality :  0.044   0.194   1087
  Planarity :  0.004   0.045   1175
  Dihedral  :  4.686  43.485    975
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  9.75 %
    Favored  : 90.14 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 20.54 %
    Favored  : 76.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.14 (0.29), residues: 872
  helix:  1.56 (0.40), residues: 170
  sheet: -0.43 (0.33), residues: 257
  loop : -1.96 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 224 
 TYR   0.024   0.001   TYR A 321 
 PHE   0.014   0.002   PHE C 226 
 TRP   0.011   0.001   TRP C 171 
 HIS   0.003   0.001   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 6734)
  covalent geometry    : angle       0.65860 ( 9222)
  SS BOND              : bond        0.00403 (    4)
  SS BOND              : angle       0.73727 (    8)
  hydrogen bonds       : bond        0.03074 (  249)
  hydrogen bonds       : angle       5.23865 (  678)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.221 
Fit side-chains
REVERT: R  118 GLN cc_start: 0.8856 (tp40) cc_final: 0.8515 (tp40)
REVERT: R  122 PHE cc_start: 0.9018 (m-10) cc_final: 0.8421 (m-80)
REVERT: R  183 ASN cc_start: 0.7814 (m-40) cc_final: 0.7248 (p0)
REVERT: R  188 TYR cc_start: 0.5914 (OUTLIER) cc_final: 0.4663 (t80)
REVERT: R  229 LEU cc_start: 0.4215 (tp) cc_final: 0.3914 (mt)
REVERT: A  129 LEU cc_start: 0.7714 (mt) cc_final: 0.7275 (mt)
  outliers start: 16
  outliers final: 14
  residues processed: 106
  average time/residue: 0.0559
  time to fit residues: 8.9139
Evaluate side-chains
  108 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  188 TYR
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain A residue   49 LYS
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   54 TYR
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   38 GLN
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue   83 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 3 optimal weight:    5.9990
   chunk 85 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 61 optimal weight:    0.5980
   chunk 67 optimal weight:    0.0570
   chunk 20 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9990
   chunk 29 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.6698

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 162 ASN
B  73 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4463 r_free = 0.4463 target = 0.187529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.152209 restraints weight = 10071.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.4077 rms_B_bonded: 3.50
r_work: 0.3783 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.3234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6738  Z= 0.132
  Angle     :  0.652  10.760   9230  Z= 0.322
  Chirality :  0.044   0.203   1087
  Planarity :  0.004   0.046   1175
  Dihedral  :  4.656  45.962    975
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  9.52 %
    Favored  : 90.37 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 20.70 %
    Favored  : 76.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.14 (0.29), residues: 872
  helix:  1.58 (0.40), residues: 170
  sheet: -0.42 (0.33), residues: 257
  loop : -1.97 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 224 
 TYR   0.019   0.001   TYR A 321 
 PHE   0.013   0.001   PHE R  62 
 TRP   0.011   0.001   TRP C 171 
 HIS   0.003   0.001   HIS A 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6734)
  covalent geometry    : angle       0.65190 ( 9222)
  SS BOND              : bond        0.00388 (    4)
  SS BOND              : angle       0.70680 (    8)
  hydrogen bonds       : bond        0.02963 (  249)
  hydrogen bonds       : angle       5.11644 (  678)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.262 
Fit side-chains
REVERT: R  118 GLN cc_start: 0.8854 (tp40) cc_final: 0.8530 (tp40)
REVERT: R  122 PHE cc_start: 0.8981 (m-10) cc_final: 0.8396 (m-80)
REVERT: R  183 ASN cc_start: 0.7804 (m-40) cc_final: 0.7264 (p0)
REVERT: R  188 TYR cc_start: 0.5864 (OUTLIER) cc_final: 0.4666 (t80)
REVERT: R  213 ILE cc_start: 0.7216 (mm) cc_final: 0.6884 (mt)
REVERT: R  229 LEU cc_start: 0.4174 (tp) cc_final: 0.3875 (mt)
REVERT: C  214 ASP cc_start: 0.7187 (m-30) cc_final: 0.6899 (m-30)
  outliers start: 18
  outliers final: 13
  residues processed: 111
  average time/residue: 0.0523
  time to fit residues: 8.9259
Evaluate side-chains
  105 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  188 TYR
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain A residue   49 LYS
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   54 TYR
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   38 GLN
Chi-restraints excluded: chain C residue   66 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 4 optimal weight:    8.9990
   chunk 58 optimal weight:   10.0000
   chunk 46 optimal weight:    0.4980
   chunk 66 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 72 optimal weight:    4.9990
   overall best weight:    1.8386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 162 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.186203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.141323 restraints weight = 10235.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.3949 rms_B_bonded: 2.72
r_work: 0.3779 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.3546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063   6738  Z= 0.232
  Angle     :  0.733  10.270   9230  Z= 0.371
  Chirality :  0.047   0.195   1087
  Planarity :  0.005   0.046   1175
  Dihedral  :  4.893  37.184    975
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 10.78 %
    Favored  : 88.99 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 22.13 %
    Favored  : 75.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.29), residues: 872
  helix:  1.47 (0.40), residues: 170
  sheet: -0.57 (0.32), residues: 263
  loop : -2.07 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 224 
 TYR   0.035   0.002   TYR A 321 
 PHE   0.018   0.002   PHE A  61 
 TRP   0.014   0.002   TRP C 171 
 HIS   0.006   0.001   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00553 ( 6734)
  covalent geometry    : angle       0.73299 ( 9222)
  SS BOND              : bond        0.00531 (    4)
  SS BOND              : angle       0.90839 (    8)
  hydrogen bonds       : bond        0.03433 (  249)
  hydrogen bonds       : angle       5.43911 (  678)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: R  118 GLN cc_start: 0.8886 (tp40) cc_final: 0.8231 (tp40)
REVERT: R  122 PHE cc_start: 0.9021 (m-10) cc_final: 0.8110 (m-80)
REVERT: R  183 ASN cc_start: 0.7734 (m-40) cc_final: 0.7148 (p0)
REVERT: R  229 LEU cc_start: 0.4273 (tp) cc_final: 0.3963 (mt)
  outliers start: 17
  outliers final: 13
  residues processed: 109
  average time/residue: 0.0502
  time to fit residues: 8.2293
Evaluate side-chains
  108 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  188 TYR
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain A residue   49 LYS
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   54 TYR
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain C residue   38 GLN
Chi-restraints excluded: chain C residue   66 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 22 optimal weight:   20.0000
   chunk 20 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 14 optimal weight:    9.9990
   chunk 75 optimal weight:    1.9990
   chunk 5 optimal weight:    9.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.185642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.148290 restraints weight = 10105.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.4028 rms_B_bonded: 4.00
r_work: 0.3690 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.3572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   6738  Z= 0.183
  Angle     :  0.708  10.472   9230  Z= 0.355
  Chirality :  0.046   0.208   1087
  Planarity :  0.005   0.046   1175
  Dihedral  :  4.868  39.488    975
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  9.98 %
    Favored  : 89.79 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 22.13 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.29), residues: 872
  helix:  1.49 (0.40), residues: 170
  sheet: -0.60 (0.32), residues: 263
  loop : -2.04 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 224 
 TYR   0.028   0.002   TYR A 321 
 PHE   0.014   0.002   PHE A  61 
 TRP   0.012   0.002   TRP C 171 
 HIS   0.003   0.001   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 6734)
  covalent geometry    : angle       0.70816 ( 9222)
  SS BOND              : bond        0.00484 (    4)
  SS BOND              : angle       0.75533 (    8)
  hydrogen bonds       : bond        0.03217 (  249)
  hydrogen bonds       : angle       5.35473 (  678)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1744 Ramachandran restraints generated.
    872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  118 GLN cc_start: 0.8880 (tp40) cc_final: 0.8494 (tp-100)
REVERT: R  122 PHE cc_start: 0.8962 (m-10) cc_final: 0.8333 (m-80)
REVERT: R  183 ASN cc_start: 0.7642 (m-40) cc_final: 0.7144 (p0)
REVERT: R  213 ILE cc_start: 0.7036 (mm) cc_final: 0.6683 (mt)
REVERT: R  229 LEU cc_start: 0.4199 (tp) cc_final: 0.3950 (mt)
REVERT: A  129 LEU cc_start: 0.7803 (mt) cc_final: 0.7273 (mt)
  outliers start: 19
  outliers final: 16
  residues processed: 110
  average time/residue: 0.0519
  time to fit residues: 8.4576
Evaluate side-chains
  109 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  188 TYR
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue 1365 LEU
Chi-restraints excluded: chain L residue  130 PHE
Chi-restraints excluded: chain A residue   49 LYS
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   54 TYR
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain C residue   38 GLN
Chi-restraints excluded: chain C residue   66 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 57 optimal weight:    9.9990
   chunk 1 optimal weight:    0.5980
   chunk 78 optimal weight:    6.9990
   chunk 0 optimal weight:    6.9990
   chunk 33 optimal weight:    0.5980
   chunk 24 optimal weight:    7.9990
   chunk 17 optimal weight:    8.9990
   chunk 20 optimal weight:    0.6980
   chunk 69 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0270
   overall best weight:    0.9840

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.186725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.151986 restraints weight = 9972.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.4069 rms_B_bonded: 3.41
r_work: 0.3714 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.3594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   6738  Z= 0.157
  Angle     :  0.691  11.179   9230  Z= 0.345
  Chirality :  0.045   0.201   1087
  Planarity :  0.004   0.046   1175
  Dihedral  :  4.760  42.442    975
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  9.86 %
    Favored  : 89.91 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 22.29 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.25 (0.29), residues: 872
  helix:  1.55 (0.40), residues: 169
  sheet: -0.58 (0.33), residues: 263
  loop : -2.01 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 224 
 TYR   0.023   0.001   TYR A 321 
 PHE   0.013   0.001   PHE C 226 
 TRP   0.013   0.001   TRP C 171 
 HIS   0.004   0.001   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 6734)
  covalent geometry    : angle       0.69094 ( 9222)
  SS BOND              : bond        0.00407 (    4)
  SS BOND              : angle       0.70442 (    8)
  hydrogen bonds       : bond        0.03114 (  249)
  hydrogen bonds       : angle       5.29121 (  678)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1759.42 seconds
wall clock time: 30 minutes 52.82 seconds (1852.82 seconds total)